Clem ate Kitty Fantastico. I'm almost certain of it. I bet there was a plan at one time to incorporate that into the storyline in season six but the writers either cut it due to all the other events they wanted to show, or they learned that the fanbase started to really like Clem, and didn't wanna anger their fans. However, Kitty mysteriously disappeared about the same time Clem started hanging around Buffy's house. So, circumstantial evidence points to Clem. He had the motive and the opportunity. It would also explain why in the season finale, when Clem took Dawn to see Ratt, Clem hightailed it and made a hasty retreat just before Dark Willow showed up, fearing that her newfound near omniscient powers would help her learn the fate of Kitty Fantastico if Clem were in her vicinity.

However, I also read a cool fanfic once that indicated Willow used Kitty as a sacrifice (similar to the use of the fawn in the season six premiere) some time before season six and after season five, as part of the preparations Willow made to get the ingredients to bring back Buffy. Had the writers gone this way, it would have further reinforced the rift between Willow & Tara, and better explained why Tara was so adamant that Willow quit magic, being a magic user herself.

Or Xander accidently stepped on it when no one was looking and then quietly disposed of the feline carcass when no one was home. The fate of Kitty Fantastico is one of the many mysteries of the Buffy series.